近期发表论文

2020
Journal Papers

1. Hongwei Huo, Xiaoyang Chen, Xu Guo, Jeffrey Scott Vitter, Efficient compression and indexing for highly repetitive DNA sequence collections, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 21 January, 2020.
2. Zhigang Sun, Hongwei Huo, Jun Huan, and Jeffrey Scott Vitter, Feature Reduction Based on Semantic Similarity for Graph Classification, Neurocomputing, to appear.

2019
Journal Papers

1. Xiaoyang Chen, Hongwei Huo, Jun Huan, and Jeffrey S. Vitter, MSQ-Index: A Succinct Index for Fast Graph Similarity Search, 20 November, 2019.

2. Xiaoyang Chen, Hongwei Huo, Jun Huan, and Jeffrey S. Vitter, An efficient algorithm for graph edit distance computation, Knowledge-Based Systems,163(2019): 762–775, 2019.

2018
Journal Papers

1. Xiaoyang Chen, Hongwei Huo, Jun Huan, and Jeffrey S. Vitter, MSQ-Index: A Succinct Index for Fast Graph Similarity Search, arxiv.org/abs/1612.09155.

2. Xiaoyang Chen, Hongwei Huo, Jun Huan, and Jeffrey S. Vitter, An efficient algorithm for graph edit distance computation, Knowledge-Based Systems,163(2019): 762–775, 2018, https://doi.org/10.1016/j.knosys.2018.10.002.

3. Zhize Li, Jian Li and Hongwei Huo, Optimal In-Place Suffix Sorting, arxiv.org/abs/1610.08305.

4. Qiang Yu, Dingbang Wei, Hongwei Huo, SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets, BMC Bioinformatics, 2018, 19:228.

5. Zhigang Sun, Hongwei Huo, and Xiaoyang Chen, Fast Top-k Graph Similarity Search via Representative Matrices, IEEE Access, 6(3):21408- 21417, 2018.

Conference Papers

1.Hongwei Huo, Xiaoyang Chen, Yuhao Zhao, Xiaojin Zhu, and Jeffrey S. Vitter, Practical Succinct Text Indexes in External Memory, Proceedings of the IEEE Data Compression Conference (DCC), Snowbird, USA, March 27 - March 30, 2018.

2. Zhize Li, Jian Li and Hongwei Huo, Optimal In-Place Suffix Sorting, Proceedings of the 25th International Symposium on String Processing and Information Retrieval (SPIRE), Lima, Peru, October 9th –11th, 2018.

3. Zhize Li, Jian Li and Hongwei Huo, Optimal In-Place Suffix Sorting, Proceedings of Data Compression Conference (DCC), Snowbird, USA, March 27 - March 30, 2018, 422. Poster.

2017
Journal Papers

1. Xiaoyang Chen, Hongwei Huo, Jun Huan, Jeffrey S. Vitter, Efficient Graph Similarity Search in External Memory, IEEE Access, 5(1): 4551-4560, 2017.

2. Haitao Guo and Hongwei Huo, A New Algorithm for Identifying Cis-regulatory Modules Based on Hidden Markov Model, BioMed Research International, Volume 2017 (2017), Article ID 6274513, 12 pages.

2016
Journal Papers

1. Qiang Yu, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey S. Vitter and Jun Huan, RefSelect: a reference sequence selection algorithm for planted (l, d) motif search, BMC Bioinformatics, 17(Suppl 9):266, 2016.

2. Qiang Yu,Hongwei Huo and Dazheng Feng, PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets, BioMed Research International, Volume 2016, Article ID 4986707, 10 pages.
3. 霍红卫，陈晓阳，陈龙刚，于强，高阶熵压缩的全文自索引，计算机学报，39(12):2494–2511, 2016.
4. 郭海涛, 霍红卫, 于强, SegHMC: 一种基于segmental HMM模型的顺式调控模块识别算法，自动化学报, 42(11):1718–1731，2016.

Conference Papers

1.Hongwei Huo, Zhigang Sun, Shuangjiang Li, Jeffrey S. Vitter, Xinkun Wang, Qiang Yu and Jun Huan, CS2A: a compressed suffix array-based method for short read alignment, Proceedings of the IEEE Data Compression Conference (DCC), Snowbird, USA, March 29 - April 1, 2016. 271–278.

2015
Journal Papers

1. Qiang Yu, Hongwei Huo, Jeffrey S. Vitter, Jun Huan and Yakov Nekrich, An Efficient Exact Algorithm for the Motif Stem Search Problem over Large Alphabets, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 12(2):384–397, March/April 2015.
2. Qiang Yu, Hongwei Huo, Xiaoyang Chen, Haitao Guo, Jeffrey S. Vitter, and Jun Huan, An Efficient Algorithm for Discovering Motifs in Large DNA Data Sets, IEEE Transactions on NanoBioScience, 14(5):535–544, 2015.

Conference Papers

1. Hongwei Huo, Longgang Chen, Heng Zhao, Jeffrey S. Vitter, Yakov Nekrich, and Qiang Yu. A Data-Aware FM-index. ACM-SIAM Proceedings of the 17th Meeting on Algorithm Engineering and Experiments (ALENEX), San Diego, California, USA, 2015

2014
Conference Papers

1. Hongwei Huo, Longgang Chen, Jeffrey S. Vitter, and Yakov Nekrich, A Practical Implementation of Compressed Suffix Arrays with Applications to Self-indexing, Data Compression Conference (DCC), Snowbird, USA, 2014, 292–301. http://www.ittc.ku.edu/~jsv/Papers/HCV13.PracticalCSAImplementation.pdf

2. Qiang Yu, Hongwei Huo, Xiaoyang Chen, Haitao Guo, Jeffrey S. Vitter, and Jun Huan, An Efficient Motif Finding Algorithm for Large DNA Data Sets, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Belfast, UK, 2014. Student Travel Award.

2013
Journal Papers

1. Q. Yu, H. Huo, Y. Zhang, H. Guo, and H. Guo, PairMotif+: A Fast and Effective Algorithm for De Novo Motif Discovery in DNA sequences, International Journal of Biological Sciences, 9(4):412-424, 2013.

2. Yipu Zhang, Hongwei Huo, Qiang Yu, A Heuristic Cluster-based EM Algorithm for the Planted (l, d) Problem, Journal of Bioinformatics and Computational Biology, 11(4): 1350009(19 pages), 2013.

3. 张懿璞, 霍红卫, 于强, 郭鸿志, 用于转录因子结合位点识别的定位投影求精算法, 计算机学报, Vol. 36, No.12, pp. 2545–2559, 2013.

Conference Papers

1. Q. Yu, H. Huo, J. S. Vitter, J. Huan and Y. Nekrich, StemFinder: An Efficient Algorithm for Searching Motif Stems over Large Alphabets, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shanghai, pages 473-476, 2013.

2012
Journal Papers

1. Yu Q, Huo H, Zhang Y, and Guo H, PairMotif: A New Pattern-driven Algorithm for Planted (l, d) DNA Motif Search, PLoS ONE, 7(10): e48442, 2012. 

2. 霍红卫, 郭丹丹, 于强等, (l, d)-模体识别问题的遗传优化算法，计算机学报, Vol. 35, No. 7, pp.1429–1439, 2012.

Conference Papers

1. H. Huo, S. Lin, Q. Yu, Y. Zhang, and V. Stojkovic, A MapReduce-based Algorithm for Motif Search, 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Shanghai, pages 2052-2060, 2012.

2010
Journal Papers

1. Hongwei Huo, Zhenhua Zhao, V. Stojkovic, Optimizing Genetic Algorithm for Motif Discovery, Mathematical and Computer Modelling, 52(11–12): 2011-2020, 2010.